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feat: fsspec for all non-object writing - %-encoded urls no longer de…
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…coded (#1034)

* writing goes through fsspec

* increase rc version

* type hints and docs

* add helper methods, create

* throw more specific error

* add additional test for `create` failure with scheme other than local

* simplify source selection

* remove windows specific code

* raise exception if invalid combination of handler / input (file-like object and fsspec)

* use softer check for file-like object

* cover problematic case with additional slash (file:///c:/file.root)

* test "file:" scheme (no slash)

* test backslash
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lobis committed Dec 5, 2023
1 parent d4d953b commit 83b0ae1
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Showing 9 changed files with 225 additions and 292 deletions.
139 changes: 49 additions & 90 deletions src/uproot/_util.py
Original file line number Diff line number Diff line change
Expand Up @@ -12,17 +12,20 @@
import itertools
import numbers
import os
import platform
import re
import warnings
from collections.abc import Iterable
from urllib.parse import unquote, urlparse
from pathlib import Path
from typing import IO
from urllib.parse import urlparse

import fsspec
import numpy
import packaging.version

win = platform.system().lower().startswith("win")
import uproot.source.chunk
import uproot.source.fsspec
import uproot.source.object


def tobytes(array):
Expand All @@ -36,7 +39,7 @@ def tobytes(array):
return array.tostring()


def isint(x):
def isint(x) -> bool:
"""
Returns True if and only if ``x`` is an integer (including NumPy, not
including bool).
Expand All @@ -46,7 +49,7 @@ def isint(x):
)


def isnum(x):
def isnum(x) -> bool:
"""
Returns True if and only if ``x`` is a number (including NumPy, not
including bool).
Expand All @@ -56,7 +59,7 @@ def isnum(x):
)


def ensure_str(x):
def ensure_str(x) -> str:
"""
Ensures that ``x`` is a string (decoding with 'surrogateescape' if necessary).
"""
Expand Down Expand Up @@ -94,18 +97,17 @@ def is_file_like(
obj, readable: bool = False, writable: bool = False, seekable: bool = False
) -> bool:
return (
callable(getattr(obj, "read", None))
and callable(getattr(obj, "write", None))
and callable(getattr(obj, "seek", None))
and callable(getattr(obj, "tell", None))
and callable(getattr(obj, "flush", None))
all(
callable(getattr(obj, attr, None))
for attr in ("read", "write", "seek", "tell", "flush")
)
and (not readable or not hasattr(obj, "readable") or obj.readable())
and (not writable or not hasattr(obj, "writable") or obj.writable())
and (not seekable or not hasattr(obj, "seekable") or obj.seekable())
)


def parse_version(version):
def parse_version(version: str):
"""
Converts a semver string into a Version object that can be compared with
``<``, ``>=``, etc.
Expand All @@ -116,7 +118,7 @@ def parse_version(version):
return packaging.version.parse(version)


def from_module(obj, module_name):
def from_module(obj, module_name: str) -> bool:
"""
Returns True if ``obj`` is an instance of a class from a module
given by name.
Expand Down Expand Up @@ -155,7 +157,7 @@ def _regularize_filter_regex_flags(flags):
return flagsbyte


def no_filter(x):
def no_filter(x) -> bool:
"""
A filter that accepts anything (always returns True).
"""
Expand Down Expand Up @@ -285,10 +287,6 @@ def regularize_path(path):
return path


_windows_drive_letter_ending = re.compile(r".*\b[A-Za-z]$")
_windows_absolute_path_pattern = re.compile(r"^[A-Za-z]:[\\/]")
_windows_absolute_path_pattern_slash = re.compile(r"^[\\/][A-Za-z]:[\\/]")

# These schemes may not appear in fsspec if the corresponding libraries are not installed (e.g. s3fs)
_remote_schemes = ["root", "s3", "http", "https"]
_schemes = list({*_remote_schemes, *fsspec.available_protocols()})
Expand Down Expand Up @@ -324,87 +322,48 @@ def file_object_path_split(urlpath: str) -> tuple[str, str | None]:
return urlpath, obj


def file_path_to_source_class(file_path, options):
def file_path_to_source_class(
file_path_or_object: str | Path | IO, options: dict
) -> tuple[type[uproot.source.chunk.Source], str | IO]:
"""
Use a file path to get the :doc:`uproot.source.chunk.Source` class that would read it.
Returns a tuple of (class, file_path) where the class is a subclass of :doc:`uproot.source.chunk.Source`.
"""

import uproot.source.chunk

file_path = regularize_path(file_path)
file_path_or_object: str | IO = regularize_path(file_path_or_object)

source_cls = options["handler"]
if source_cls is not None:
if not (
isinstance(source_cls, type)
and issubclass(source_cls, uproot.source.chunk.Source)
if source_cls is not None and not (
isinstance(source_cls, type)
and issubclass(source_cls, uproot.source.chunk.Source)
):
raise TypeError(
f"'handler' is not a class object inheriting from Source: {source_cls!r}"
)

# Infer the source class from the file path
if all(
callable(getattr(file_path_or_object, attr, None)) for attr in ("read", "seek")
):
# need a very soft object check for ubuntu python3.8 pyroot ci tests, cannot use uproot._util.is_file_like
if (
source_cls is not None
and source_cls is not uproot.source.object.ObjectSource
):
raise TypeError(
f"'handler' is not a class object inheriting from Source: {source_cls!r}"
f"'handler' is not ObjectSource for a file-like object: {source_cls!r}"
)
return source_cls, file_path

if (
not isinstance(file_path, str)
and hasattr(file_path, "read")
and hasattr(file_path, "seek")
):
source_cls = uproot.source.object.ObjectSource
return source_cls, file_path

windows_absolute_path = None
if win and _windows_absolute_path_pattern.match(file_path) is not None:
windows_absolute_path = file_path

parsed_url = urlparse(file_path)
if parsed_url.scheme.lower() == "file":
parsed_url_path = unquote(parsed_url.path)
return uproot.source.object.ObjectSource, file_path_or_object
elif isinstance(file_path_or_object, str):
source_cls = (
uproot.source.fsspec.FSSpecSource if source_cls is None else source_cls
)
return source_cls, file_path_or_object
else:
parsed_url_path = parsed_url.path

if win and windows_absolute_path is None:
if _windows_absolute_path_pattern.match(parsed_url_path) is not None:
windows_absolute_path = parsed_url_path
elif _windows_absolute_path_pattern_slash.match(parsed_url_path) is not None:
windows_absolute_path = parsed_url_path[1:]

scheme = parsed_url.scheme.lower()
if (
scheme == "file"
or len(parsed_url.scheme) == 0
or windows_absolute_path is not None
):
if windows_absolute_path is None:
if parsed_url.netloc.lower() == "localhost":
file_path = parsed_url_path
else:
file_path = parsed_url.netloc + parsed_url_path
else:
file_path = windows_absolute_path

# uproot.source.file.MemmapSource
source_cls = uproot.source.fsspec.FSSpecSource

return source_cls, os.path.expanduser(file_path)

elif scheme == "root":
# uproot.source.xrootd.XRootDSource
source_cls = uproot.source.fsspec.FSSpecSource
return source_cls, file_path

elif scheme == "s3":
# uproot.source.s3.S3Source
source_cls = uproot.source.fsspec.FSSpecSource
return source_cls, file_path

elif scheme in ("http", "https"):
# uproot.source.http.HTTPSource
source_cls = uproot.source.fsspec.FSSpecSource
return source_cls, file_path

return uproot.source.fsspec.FSSpecSource, file_path
raise TypeError(
f"file_path is not a string or file-like object: {file_path_or_object!r}"
)


if isinstance(__builtins__, dict):
Expand Down Expand Up @@ -448,7 +407,7 @@ def _file_not_found(files, message=None):
)


def memory_size(data, error_message=None):
def memory_size(data, error_message=None) -> int:
"""
Regularizes strings like '## kB' and plain integer number of bytes to
an integer number of bytes.
Expand Down Expand Up @@ -739,7 +698,7 @@ def damerau_levenshtein(a, b, ratio=False):
# Modified Damerau-Levenshtein distance. Adds a middling penalty
# for capitalization.
# https://en.wikipedia.org/wiki/Damerau%E2%80%93Levenshtein_distance
M = [[0] * (len(b) + 1) for i in range(len(a) + 1)]
M = [[0] * (len(b) + 1) for _ in range(len(a) + 1)]

for i in range(len(a) + 1):
M[i][0] = i
Expand Down Expand Up @@ -771,7 +730,7 @@ def damerau_levenshtein(a, b, ratio=False):
# Transpose only
M[i][j] = min(M[i][j], M[i - 2][j - 2] + 1)
else:
# Traspose and capitalization
# Transpose and capitalization
M[i][j] = min(M[i][j], M[i - 2][j - 2] + 1.5)

if not ratio:
Expand Down
6 changes: 5 additions & 1 deletion src/uproot/reading.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,14 @@
"""
from __future__ import annotations

from __future__ import annotations

import struct
import sys
import uuid
from collections.abc import Mapping, MutableMapping
from pathlib import Path
from typing import IO

import uproot
import uproot.behaviors.TBranch
Expand Down Expand Up @@ -525,7 +529,7 @@ class ReadOnlyFile(CommonFileMethods):

def __init__(
self,
file_path,
file_path: str | Path | IO,
*,
object_cache=100,
array_cache="100 MB",
Expand Down
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